Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of proteins and miRNAs that specifically bind an mRNA in vivo

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE130733 | GEO | 2019/08/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification of proteins and miRNAs that specifically bind an mRNA in vivo.

Project description:Understanding regulation of an mRNA requires knowledge of its regulators. However, methods for reliable de-novo identification of proteins binding to a particular RNA are scarce and were thus far only successfully applied to abundant noncoding RNAs in cell culture. Here, we present vIPR, an RNA-protein crosslink, RNA pulldown, and shotgun proteomics approach to identify proteins bound to selected mRNAs in C. elegans. Applying vIPR to the germline-specific transcript gld-1 led to enrichment of known and novel interactors. By comparing enrichment upon gld-1 and lin-41 pulldown, we demonstrate that vIPR recovers both common and specific RNA-binding proteins, and we validate DAZ-1 as a specific gld-1 regulator. Finally, combining vIPR with small RNA sequencing, we recover known and biologically important transcript-specific miRNA interactions, and we identify miR-84 as a specific interactor of the gld-1 transcript. We envision that vIPR will provide a platform for investigating RNA in vivo regulation in diverse biological systems.

| S-EPMC6746756 | biostudies-literature

Identification of proteins and miRNAs that specifically bind an mRNA in vivo

Project description:Understanding regulation of an mRNA requires knowledge of its regulators. However, methods for reliable de-novo identification of proteins binding to a particular RNA are scarce and were so far only successfully applied to abundant noncoding RNAs in cell culture. Here, we present vIPR, an RNA-protein crosslink, RNA pulldown, and shotgun proteomics approach to identify proteins bound to a selected mRNA in C. elegans. Applying vIPR to the germline-specific transcript gld-1 led to enrichment of known and novel interactors. By comparing enrichment upon gld-1 and lin-41 pulldown, we demonstrate that vIPR recovers both common and specific RNA-binding proteins, and we validate DAZ-1 as a novel and specific gld-1 regulator. Finally, combining vIPR with small RNA sequencing, we recover known and biologically important transcript-specific miRNA interactions, and we identify miR-84 as a specific interactor of the gld-1 transcript. We envision that vIPR provides a platform for investigating RNA in vivo regulation in diverse biological systems.

2019-08-12 | PXD013720 | Pride

Identification of proteins and miRNAs that specifically bind an mRNA in vivo [total RNA]

Project description:Understanding regulation of an mRNA requires knowledge of its regulators. However, methods for reliable de-novo identification of proteins binding to a particular RNA are scarce and were so far only successfully applied to abundant noncoding RNAs in cell culture. Here, we present vIPR, an RNA-protein crosslink, RNA pulldown, and shotgun proteomics approach to identify proteins bound to a selected mRNA in C. elegans. Applying vIPR to the germline-specific transcript gld-1 led to enrichment of known and novel interactors. By comparing enrichment upon gld-1 and lin-41 pulldown, we demonstrate that vIPR recovers both common and specific RNA-binding proteins, and we validate DAZ-1 as a novel and specific gld-1 regulator. Finally, combining vIPR with small RNA sequencing, we recover known and biologically important transcript-specific miRNA interactions, and we identify miR-84 as a specific interactor of the gld-1 transcript. We envision that vIPR provides a platform for investigating RNA in vivo regulation in diverse biological systems.

2019-08-08 | GSE130730 | GEO

Identification of proteins and miRNAs that specifically bind an mRNA in vivo [small RNA]

Project description:Understanding regulation of an mRNA requires knowledge of its regulators. However, methods for reliable de-novo identification of proteins binding to a particular RNA are scarce and were so far only successfully applied to abundant noncoding RNAs in cell culture. Here, we present vIPR, an RNA-protein crosslink, RNA pulldown, and shotgun proteomics approach to identify proteins bound to a selected mRNA in C. elegans. Applying vIPR to the germline-specific transcript gld-1 led to enrichment of known and novel interactors. By comparing enrichment upon gld-1 and lin-41 pulldown, we demonstrate that vIPR recovers both common and specific RNA-binding proteins, and we validate DAZ-1 as a novel and specific gld-1 regulator. Finally, combining vIPR with small RNA sequencing, we recover known and biologically important transcript-specific miRNA interactions, and we identify miR-84 as a specific interactor of the gld-1 transcript. We envision that vIPR provides a platform for investigating RNA in vivo regulation in diverse biological systems.

2019-08-08 | GSE130732 | GEO

Identification of proteins and miRNAs that specifically bind an mRNA in vivo

Project description:Identification of proteins and miRNAs that specifically bind an mRNA in vivo

| PRJNA541231 | ENA

Identification of proteins and miRNAs that specifically bind an mRNA in vivo [total RNA]

Project description:Identification of proteins and miRNAs that specifically bind an mRNA in vivo [total RNA]

| PRJNA541233 | ENA

Identification of proteins and miRNAs that specifically bind an mRNA in vivo [small RNA]

Project description:Identification of proteins and miRNAs that specifically bind an mRNA in vivo [small RNA]

| PRJNA541234 | ENA

Combinatorial mRNA Regulation by miRNAs and Pumilio proteins

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-10-17 | GSE110520 | GEO

Identification of miRNAs that regulate Colorectal Cancer Metastasis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-01-15 | E-GEOD-56320 | biostudies-arrayexpress

Identification of nuclear-enriched miRNAs during mouse granulopoiesis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-05-14 | E-GEOD-57624 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data